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Rui Fu

RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus

I have studied various aspects of RNA-related gene expression regulation processes, including transcription, translation, and especially RNA degradation. In lieu of 10 years of bench research experience, I have now worked several years in bioinformatic roles analyzing high throughput sequencing data.

Education

Ph.D. Biological Science

University of California San Diego

La Jolla, CA

2015 - 2009

B.S. Biological Science

Xiamen University

Xiamen, China

2009 - 2005

Research Experience

Bioinformatic tool development: 1) clustifyr, single cell RNA-seq cell identity assignment (author); 2) valr, tidyverse-style genomic interval analysis (co-developer); 3) scraps, extraction of polyadenylation site info from scRNA-seq data (co-developer); 4) squirrelBox, RNA-seq data visualization and analysis browser using Shiny (author)

Postdoctoral Informatics Fellow

Jay Hesselberth’s Supervision

University of Colorado Anschutz

Current - 2017

  • Development of bioinformatics software packages
  • RNA-seq and transcriptome improvements for hiberating ground squirrel brain regions
  • Informatics support on various RNA biology collaborations, analyzing genomic and sequencing data

Postdoctoral Research Fellow

Judy Lieberman’s Lab

Harvard Medical School

2017 - 2016

  • Identification of the mitochondrial trigger of apoptotic mRNA decay
  • Purificiation of cytotoxic granules and key cytolytic molecules by fast protein liquid chromatography
  • Mouse gene manipulation by CRISPR-Cas9, and genotyping with R scripts

Graduate Research Assistant

Jens Lykke-Andersen’s Lab

University of California San Diego

2015 - 2009

  • Investigation of co-factors involved in ZFP36(TTP)-mediated mRNA decay and translational repression during the immune response of macrophages
  • Characterization of the roles of ZFP36 family proteins in cell cycle progression regulation of mouse embryonic fibroblasts

Undergraduate Research Assistant

Ruichuan Chen’s Lab

Xiamen University

2009 - 2007

  • Exploration of cell cycle and apoptosis implications of the transcription elongation regulator HEXIM1
  • Mechanistic characterization of p-TEFb activation by HIV-Tat




Teaching Experience

Lecture Instructor (Graduate Level Courses)

University of Colorado Anschutz

N/A

Current - 2018

  • Lecture for RNA sequencing section of Rigor in Research (2020)
  • Lectures, paper discussion, and exam/homework design for RNA section of Foundations in Biomedical Sciences (2018, 2019)
  • Lectures for Practical Data Analysis with R/RStudio (2018, 2019)
  • Workshop for scRNA-seq Data Analysis (2019)

Teaching Assistant (Graduate Level Courses)

University of Colorado Anschutz

N/A

Current - 2019

  • Practical Computational Biology for Biologists: R
  • Practical Computational Biology for Biologists: Python

RNA Bioscience Initiative Informatics Office Hour (weekly)

University of Colorado Anschutz

N/A

Current - 2018

RNA Bioscience Initiative Summer Internship Mentoring

University of Colorado Anschutz

N/A

2020

  • Mentoring of undergraduate summer research, systemically exploring scRNA-seq cell type signatures

Summer Research Mentoring

Harvard Medical School

N/A

2017

  • Mentoring of bench/informatics research and scientific writing for high school student enrolled in the MIT Research Science Institute program

BS/MS Student Research Mentoring

University of California San Diego

N/A

2015 - 2013

  • Mentoring of student research for undergraduate honor thesis and master thesis projects
  • Mentee was awarded best poster presentation at 2014 Biological Sciences Annual Student Research Showcase

Teaching Assistant (Undergraduate)

University of California San Diego

N/A

2012 - 2011

  • Molecular Biology
  • DNA Recombination Lab

Publications, as First Author

tinyurl.com/googlescholar-rf

mRNA processing in the brain of a heterothermic mammal during hibernation

In preparation for submission

N/A

2020

  • Gillen A*, Fu R*, Riemondy K, Hesselberth J, Martin, S.

clustifyr: an R package for automated single-cell RNA sequencing cluster classification

F1000Research

N/A

2020

  • Fu R, Gillen A, Sheridan R, Tian C, Daya M, Hao Y, Hesselberth J, Riemondy K.

PNPT1 release from mitochondria during apoptosis triggers decay of poly(A) RNAs

Cell

N/A

2018

  • Liu X*, Fu R*, Pan Y, Meza-Sosa K, Zhang Z, Lieberman J.

Recruitment of the 4EHP-GYF2 cap-binding complex to tetraproline motifs of tristetraprolin promotes repression and degradation of mRNAs with AU-rich elements

RNA

N/A

2016

  • Fu R, Olsen MT, Webb K, Bennett EJ, Lykke-Andersen J.

Publications, as Contributing Author

Monocytic Subclones Confer Resistance to Venetoclax-Based Therapy in Acute Myeloid Leukemia Patients

Cancer Discovery

N/A

2019

  • Pei S, Pollyea D, Gustafson A, Stevens B, Minhajuddin M, Fu R, Riemondy K, Gillen A, Sheridan R, Kim J, Costello J, Amaya M, Inguva A, Winters A, Ye H, Krug A, Jones C, Adane B, Khan N, Ponder J, Schowinsky J, Abbott D, Hammes A, Myers J, Ashton J, Nemkov T, D’Alessandro A, Gutman J, Fesik S, Ramsey H, Savona M, Smith C, Jordan C.

Chronic Liver Disease in Humans Causes Expansion and Differentiation of Liver Lymphatic Endothelial Cells

Frontiers in Immunology

N/A

2019

  • Tamburini, BAJ, Finlon JM, Gillen A, Kriss MS, Riemondy K, Fu R, Schuyler R, Hesselberth J, Rosen HR, Burchill MA.

Single cell RNA Sequencing Identifies Transforming Growth Factor ß as a Critical Regulator of Alveolar Regeneration

JCI Insight

N/A

2019

  • Riemondy K, Jansing N, Jiang P, Redente E, Gillen A, Fu R, Anthony G, Hesselberth J, Zemans R.

Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries.

Nucleic Acid Research

N/A

2019

  • Riemondy K, Ransom M, Alderman C, Gillen A, Fu R, Finlay-Schultz J, Kirkpatrick G, Di Paola J, Kabos P, Sartorius C, Hesselberth J.

Posters and Talks

ClustifyR: automated single-cell RNA sequencing cluster classification

Keystone Symposia on Single Cell Biology (Poster)

N/A

2019

PNPT1 release from the mitochondrial intermembrane space triggers rapid decay of mRNA and poly(A)-tailed ncRNA during apoptosis

Boston Children’s Hospital PCMM Research Poster Session (Poster)

N/A

2017

PNPT1 release from the mitochondrial intermembrane space triggers rapid decay of mRNA during apoptosis

2016 Boston Children’s Hospital PCMM Research Poster Session (Poster)

N/A

2016

TTP-mediated mRNA repression involves recruitment of the 4EHP-GYF2 complex

Cold Spring Harbor Laboratory mRNA Processing Meeting (Presentation)

N/A

2015

TTP represses translation of target mRNAs through the 4EHP-GYF2 complex

UCSD Mechanisms of Gene Expression Seminar (Presentation)

N/A

2014

TTP family proteins regulate the stability of retinoblastoma protein mRNAs during serum-stimulated G0-S transition

Cold Spring Harbor Laboratory mRNA Processing Meeting (Poster)

N/A

2013

The regulation of TTP family mRNA-decay factors during G0-S cell cycle progression

Keystone Symposia on Protein-RNA Interactions (Poster)

N/A

2012

Service, Training, Recognition

Society memberships: RNA Society, International Society for Computational Biology, Genetics Society of America

GENETICS Early Career Reviewer

N/A

N/A

Current - 2018

Peer review of manuscripts under Dr Lykke-Andersen, Dr Lieberman, Dr Hesselberth

N/A

N/A

Current - 2011

Admissions Committee Member for CU Graduate Experiences for Multicultural Students

N/A

N/A

2019

Mentor for CU-Anschutz ISCORE undergraduate mentorship program

N/A

N/A

2019

BioFrontiers Hackathon

N/A

N/A

2018

Data Incubator Data Science Fellowship

N/A

N/A

2017

Harvard Medical School Scientists Teaching Science Course

N/A

N/A

2016

Organizer for UCSD Ethics Center’s Silent Spring Project

N/A

N/A

2012

Dr Huang Memorial Scholarship

N/A

N/A

2011 - 2009

National College Students Creativity Experiment Project

N/A

N/A

2009 - 2007

University Merit Student, First-Class Scholarship

N/A

N/A

2008 - 2006

Disclaimer

Made with pagedown.

github.com/raysinensis/cv.

Last updated on 2020-05-19.